<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
<title>Brainstorm</title>
<link href='http://fonts.googleapis.com/css?family=Molengo'
	rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Hammersmith+One'
	rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Alice'
	rel='stylesheet' type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Ovo' rel='stylesheet'
	type='text/css'>
<link href='http://fonts.googleapis.com/css?family=Federo'
	rel='stylesheet' type='text/css'>

<link href="modeling.css" rel="stylesheet" type="text/css">

<link href="global.css" rel="stylesheet" type="text/css">

<link href="template2.css" rel="stylesheet" type="text/css"><!-- include the Tools -->
<script src="http://cdn.jquerytools.org/1.2.6/full/jquery.tools.min.js"></script>

<style type="text/css">
</style>
</head>

<body>
<div class="global">

<div id=top2></div>

<div class="header">
<div class="bgimg"></div>
<div class="bgpart1"></div>
<div class="bgpart2"></div>


<div class="banner">
<div class="logo"><img
	src="http://2011.igem.org/wiki/images/c/c9/Logo.png" width="200"
	height="200" /></div>
<div class="title"><img
	src="http://ung.igem.org/wiki/images/b/b3/Title.png" width="603"
	height="220" /></div>
<div class="igemlogo"><a target="_blank"
	href="http://2011.igem.org"><img
	src="http://2011.igem.org/wiki/images/e/e2/Igemlogo.png" width="180"
	height="150" /></a></div>
</div>
<!--banner-->
<div class="nav">
<ul id="topnav">
	<li><a id="P_Home" href="http://zjuchina.tk/index.html">Home</a></li>

	<li><a id="P_Project"
		href="http://zjuchina.tk/Project.html">Project</a> <!--Subnav Starts Here-->


	<!--Subnav Ends Here--></li>
	<li><a id="P_Team" href="http://zjuchina.tk/Team.html">Team</a>

	</li>
	<li><a id="P_Notebook"
		href="http://zjuchina.tk/Notebook.html">Notebook</a></li>
	<li><a id="P_HumanPractice"
		href="http://zjuchina.tk/Humanpractice.html">HumanPractice</a>
	</li>
	<li id="search">
	<div id="searchbar">

	<div>
	<form action="http://www.google.com.hk/cse" id="cse-search-box"
		target="_blank">
	<div><input type="hidden" name="cx"
		value="005438704919531788579:zbfi5n-q5du" /> <input type="hidden"
		name="cof" value="FORID:10" /> <input type="hidden" name="ie"
		value="UTF-8" /> <input type="text" name="q" size="15" /> <input
		type="submit" name="sa" value="Search" /></div>
	</form>
	<script type="text/javascript"
		src="http://www.google.com/cse/brand?form=cse-search-box&lang=en"></script></div>
	</div>
	</li>
</ul>
</div>
<!--navbar--> <script type="text/javascript">
   document.getElementById('P_Team').onclick=function(){
	   document.getElementById('P_Te').style.display='block'

	    document.getElementById('P_Pr').style.display='none'
		document.getElementById('P_No').style.display='none'
		document.getElementById('P_Hu').style.display='none'
		<!-- document.getElementById('P_Pr').style.display='none' -->
	   };
	    document.getElementById('P_Project').onclick=function(){
	   document.getElementById('P_Pr').style.display='block'
	    document.getElementById('P_Te').style.display='none'
		document.getElementById('P_No').style.display='none'
		document.getElementById('P_Hu').style.display='none'
		<!-- document.getElementById('P_Pr').style.display='none' -->
	   };
	    document.getElementById('P_Notebook').onclick=function(){
	   document.getElementById('P_No').style.display='block'
	    document.getElementById('P_Pr').style.display='none'
		document.getElementById('P_Te').style.display='none'
		document.getElementById('P_Hu').style.display='none'
		<!-- document.getElementById('P_Pr').style.display='none' -->
	   };
	    document.getElementById('P_HumanPractice').onclick=function(){
	   document.getElementById('P_Hu').style.display='block'
	    document.getElementById('P_Pr').style.display='none'
		document.getElementById('P_No').style.display='none'
		document.getElementById('P_Te').style.display='none'
		<!-- document.getElementById('P_Pr').style.display='none' -->
	   };
	  
</script></div>
<!--header-->
<div id="contentwrapper">

<div class="main">

<div class="bgpart3"></div>
<div class="leftulcontainer" id="blue">
<div id="leftul" class="leftul">
<div id="accordion">

<h4>Lab Notes</h4>

<div class="pane"><a
	href="http://zjuchina.tk/Notebook.html">July</a> <a
	href="http://zjuchina.tk/August.html">August<br />
</a> <a href="http://zjuchina.tk/September.html">September<br />
</a></div>

<h4>Protocol</h4>

<div class="pane"><a
	href="http://zjuchina.tk/Protocol.html">Protocol</a></div>
<h4 class="current">Brainstorm</h4>
<div class="pane" style="display: block;"><a
	href="http://zjuchina.tk/Brainstorm.html">Brainstorm</a></div>

<script> 
$(function() { 
 
$("#accordion").tabs("#accordion div.pane", {tabs: 'h4', effect: 'slide', initialIndex: null});
});
</script> <!-- Navigation scroll follow --> <script type="text/javascript">
        $(window).scroll(function () { 
            var scrollPos = $(window).scrollTop();
            if (scrollPos > 330) {
                $(".leftul").addClass("stickToTop");
            } else {
                $(".leftul").removeClass("stickToTop");
            }
     
        });
    </script></div>
<!--accordion--></div>
<!--leftul--></div>
<!--leftulcontainer-->

<div class="rightcontainer">
<div id="styleA" class="frame">
<div id="blue">
<p></p>
<h1>Brainstorm</h1>

<div id="framecontent">
<div class="block">
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1>Rainbofilm</h1>

</div>
</div>
</div>

<p>Biofilm has been our team's long-standing interest. Though our
motivation to study biofilm at first is on its effective elimination, a
review paper on biofilm totally changed our view of it and led us into a
new direction. When something as difficult to eliminate and natural as
biofilm is, can we make use of it instead of destroying it? Following
this strand of thought, we started to investigate the advantages brought
by the advent of biofilm for the bacteria, such as its increased
resistance to harsh conditions under which normal cells cannot survive.
Another fascinating fact about biofilm is that cells are differentially
expressed to form different layers within biofilm.</p>
<p><br />
We continued to develop our project from two ideas based on the
background. The first is based on biofilm's differentiated expression.
We hope to construct a three-layer stratified expression system within
biofilm in response to oxygen concentration gradient. This could serve
as a prototype for future construction simply by replacing the reporter
gene with user's target genes. The second idea stems from the biofilm's
strong resistance to bad growth conditions, such as when surrounded by
high concentrations of heavy metal. We want to engineer and develop our
biofilm into the second generation of biosensor. As a natural
concentration gradient of heavy metal is formed along the depth of
biofilm, with the same threshold for detection constructed in all the
cells, the whole biofilm system would be able to detect different levels
of the heavy metal concentration in its surrounding environment.</p>
</div>
<!--block-->
<div class="block" id="n_brainstorm">
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1>Gut Flora</h1>
</div>
</div>
</div>
<p>We believe engineering gut bacteria is a promising field in the
future, for bacteria are easy to be engineered compared with engineering
human cell, and human gut is naturally inhabited by many different
bacteria. We could construct a gut bacteria kit for either supplying
nutrients such as vitamins or synthesizing and delivering drugs. We're
highly motivated to do this project, for it offers a good solution to
alleviate the current famine and diseases brought by malnutrition in
many developing countries around the world. The drug delivery, adapted
to host's circadium rhythm and physiological state, would be an ideal
approach to cure some chronic diseases. However, we didn't choose to
further develop Gut Flora Kit as our team's project this year, because
we have limited knowledge and experience in gut flora and intestinal
environment.</p>
</div>
<!--block-->
<div class="block" id="n_brainstorm">
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1>Alternative Splicing</h1>
</div>
</div>
</div>

<p>Alternative splicing is a type of post-transcription mRNA
modification observed in most multi-cellular organisms. It happens where
there is more than one intron in a gene, meaning that different splicing
site choices generate different mature mRNA thus produce different
protein. The choice of the splicing site is controlled by a very complex
system, yet we have some interesting and convincing understanding about
it, and may it become a new perspective in synthetic biology.</p>
<p>In a multi-exon pre-mRNA, some exons are constitutively cut off
or maintained, while some exons are sometimes skipped and sometimes
kept. The latter is called an alternative splicing. The pattern can be
controlled by many mechanisms involving a good many RNA secondary
structure formations, protein-protein and protein-RNA interactions.
Different splicing patterns always have relatively constant expression
pattern in certain cell condition.<br />
We are inspired by this interesting phenomenon and hope to design a new
synthetic biology tool which can use compiled gene to produce many
different kinds of proteins under different conditions.</p>
<p>We are inspired by a consistent mechanism of splicing pattern
determination, which is called the mutually exclusive splicing. Every
time only one out of several exon cassettes(altering exons) are
presented. Latest discoveries revealed this is affected by certain
pre-RNA secondary structure. If we change the sequence of the regulatory
region, we may change the splicing pattern, and some proteins are
expressed in a regulated and constant way.<br />
One big problem about this idea is the chassis. Multi-cellular life-form
is not very suitable for synthetic biology, and there is no such system
in bacteria. So yeast becomes the only solution we can come up with.
Very few alternative splicing is reported in yeast, yet it can normally
carry out the pre-RNA processing function. Another is that changing the
gene sequence to control the expression pattern is too difficult to
apply.<br />
</p>
<p>Finally, we suspended this idea and tried to find other doable
and potential projects.</p>
</div>
<!--block-->
<div class="block" id="n_brainstorm">
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1>E-waste</h1>
</div>
</div>
</div>

<p>E-waste now is becoming a worldwide environmental problem.
Current treatment is like this: most countries transport the E-waste to
the developing areas; then the workers there recycle the useful or
worthy parts by hand; the useless parts are shredded and the powder
undergoes further selection by different physical and chemical
properties; eventually the remains are deeply buried. The whole process
costs tremendously and still results in environmental pollution. So we
tried to solve this problem in a synthetic biology approach.</p>
<p>We checked the components of the E waste: plastic and metal. We
continued to read related papers about bacteria degrading plastic,
mobilizing metal elements, or absorbing metal elements. Unfortunately,
the plastic substances in the E-waste like epoxy resins, and PCBs, PVC
are very hard for bacteria to degrade. Secondly, though there's some
paper indicating the power of some bacteria of recycling the metal, the
detailed mechanism is still a mystery. In order to first mobilize the
metal elements from the solid E-waste, we had proposed some ideas like
producing acid such as acetic acid, citric acid even cyanic acid, thus
the bacteria we used must be tolerant to the high pH environment. Here
the dilemma is: on one hand, if we use some special bacteria, it is
difficult to engineer it; on the other hand, if we use E.coli, it is
difficult for us to engineer it to adapt to the acid environments. Due
to these problems, we stopped further discussion on this topic.4</p>
</div>
<!--block-->
<div class="block" id="n_brainstorm">
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1 id="sm">Signal Modular by Protein Scaffold</h1>
</div>
</div>
</div>

<p>This idea comes from the paper by Keasling in which he used
protein scaffold to boost the metabolic flow in biosynthesis. We think
we can adopt similar methosd in signal transduction. At first, we were
all excited about the idea. However, the tragedy is that we found out
UCSF had done a similar project in 2007 iGEM. : (</p>
</div>
<!--block-->
<div class="block" id="n_brainstorm">
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1 id="Ch">Change the color by shaking</h1>

</div>
</div>
</div>

<p>&nbsp;This is just an interesting idea that there's no specific
practical application. The key of this idea is to discover a sensing
system based on the physical attachment between cells. So we looked up
some paper, and found one paper's novel discovery of sensing the
touching. But the fatal drawback is that it lacks detailed mechanism
that we can harness.</p>
</div>
<!--block-->
<div class="block" id="n_brainstorm">
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1 id="Sp">Streptococcus pneumonia</h1>
</div>
</div>
</div>

<p>Childhood pneumonia is the leading single cause of mortality in
children aged less than 5 years. It has been noted that Pathogenicity
islands (PAIs) plays an important role of being sickness. PAIs are a
distinct class of genomic islands and are incorporated in the genome of
pathogenic microorganisms but are usually absent from those
non-pathogenic organisms of the same or closely related species. We
would like to concentrate on the special properties of PAIs with
measures of synthetic biology. PAIs have correlation of other diseases
and may become a fundamental therapy.</p>
</div>
<!--block-->
<div class="block" id="n_brainstorm">
<div id="importantcontainer">
<div class="frame" id="important">
<div class="bgcolors" id="round">
<h1 id="AS">ASTHMA</h1>
</div>
</div>
</div>

<p>Asthma， a chronic inflammatory disease of the lungs, has been
increasingly observed in developed countries. Its remarkable increase
attributes to changes in the environment due to improved hygiene and
fewer childhood infections. Researchers have found that asthma has close
correlation with increased IgE level. Those who are prone to asthma are
able to express complete FcεRI in dendritic cell(DC). We planned to use
synthetic biology to focus on dendritic cell to lower the level of IgE
expression. This may lead to a new-era of asthma therapy and bring hope
to those suffering from asthma.</p>
</div>
<!--block-->
<p style="clear: both;"></p>

<script type="text/javascript"> 
document.getElementById('bb').onclick= function(){
document.getElementById('page2').style.display='none'
 document.getElementById('page1').style.display='block'}
 
document.getElementById('bf').onclick= function(){
	
document.getElementById('page1').style.display='none'
 document.getElementById('pgae2').style.display='block'}
</script>
<p style="clear: both"></p>
</div>
<!--framecontent-->

<div class="frame" id="rightnav" style="display: none;">
<div class="bgcolors" id="round">
<p><a name="jumptop" id="bb">&nbsp; Biobrick Group&nbsp;</a>|<a
	id="bf">&nbsp;Biofilm Group &nbsp;</a></p>
</div>
<!--bgcolors--></div>
<!--rightnav--></div>
<!--blue-->
<div class="links"><a href="#top2">Top</a></div>
</div>
<!--frame--></div>
<!--rightcontainer-->

<p style="clear: both"></p>

</div>
</div>
<!--main-->
<p style="clear: both"></p>
<div class="footer" id="footer"><a href="http://2011.igem.org/">
iGem 2011 Home Page</a> <a href="http://ung.igem.org/Special:Upload/">
Upload Files</a> <a
	href="http://2011.igem.org/wiki/index.php?title=Template:Zjucss_main&action=edit">Edit
CSS</a> <a href="http://ung.igem.org/Team_Wikis?year=2011"> Team Wikis</a> <a
	href="mailto:zjuigem@gmail.com?"><strong>Contact Us</strong></a></div>
</div>
<!--contentwrapper-->
</body>
</html>
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  